[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x

[Andreas Tille]

Hi Michiel,

thanks for testing this.  Just to let you know: I personally need to
admit that I do not feel capable to verify your test for the next couple
of weeks.

Just from my gut feling I'd say: If you find a workaround here that's
probably helpful to run the test suite successfully.

Thanks again

     Andreas.

On Sat, Aug 23, 2014 at 06:47:00PM -0700, Michiel de Hoon wrote:
> Hi Andreas,
> 
> I was able to replicate this bug on a PowerPC with Python 2.7, but only if I replace the single character into a single unicode character
> (e.g. in line 212 of test_Cluster.py, if I replace method='a' by method=u'a').
> Can you confirm that you get this bug with Python 2.7 even with simple strings rather than unicode?
> 
> Thanks,
> -Michiel.
> 
> --------------------------------------------
> On Sat, 8/16/14, Andreas Tille <andreas at an3as.eu> wrote:
> 
>  Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
>  To: "Peter Cock" <p.j.a.cock at googlemail.com>
>  Cc: "Dejan Latinovic" <Dejan.Latinovic at imgtec.com>, "Michiel de Hoon" <mjldehoon at yahoo.com>, "Biopython discussion list" <biopython at lists.open-bio.org>, "751277 at bugs.debian.org" <751277 at bugs.debian.org>, "biopython-dev at biopython.org" <biopython-dev at biopython.org>
>  Date: Saturday, August 16, 2014, 5:37 AM
>  
>  Hi Peter,
>  
>  On Thu, Aug 14, 2014 at
>  09:52:40AM +0100, Peter Cock wrote:
>  >
>  >
>  > >   1. waiting for
>  your confirmation / patch
>  >
>  >   2. deactivating the specific test
>  > >   3. exclude mips for
>  biopython
>  > >   4. ? any
>  better idea ?
>  > >
>  >
>  > In the current state all the work we spent in biopython
>  over the last
>  > > monthes will not
>  migrate to testing for the simple reason that the
>  > > current package in testing just does
>  not run the test suite at build
>  > >
>  time and moreover python3 is not supported.
>  > >
>  > > Kind
>  regards
>  > >
>  >
>  >      Andreas.
>  > 
>  > I would suggest (2), deactivate this test
>  (at least for for mips) as
>  > the most
>  practical short term solution for the Debian packages.
>  > Or if you prefer (3), don't target
>  mips for the Biopython package
>  >
>  (yet).
>  > 
>  > Medium
>  term, I hope we can fix the C code to handle either
>  > Endian platform - option (1).
>  
>  It seems after having fixed
>  the issue caused by wise we have one
>  remaining problem:
>  
>    On powerpc[1] and s390x[2] test_Cluster
>  fails even with Python 2.7 with:
>  
>  ======================================================================
>  ERROR: test_clusterdistance
>  (test_Cluster.TestCluster)
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>    File
>  "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py",
>  line 212, in test_clusterdistance
>     
>  method='a', transpose=0)
>  ValueError:
>  method should be a single character
>  
>  ======================================================================
>  ERROR: test_kcluster
>  (test_Cluster.TestCluster)
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>    File
>  "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py",
>  line 141, in test_kcluster
>     
>  method='a', dist='e')
>  ValueError: method should be a single
>  character
>  
>  ======================================================================
>  ERROR: test_somcluster
>  (test_Cluster.TestCluster)
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>    File
>  "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py",
>  line 557, in test_somcluster
>     
>  inittau=0.02, niter=100, dist='e')
>  ValueError: distance should be a single
>  character
>  
>  ======================================================================
>  ERROR: test_treecluster
>  (test_Cluster.TestCluster)
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>    File
>  "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py",
>  line 290, in test_treecluster
>     
>  transpose=0, method='a', dist='e')
>  ValueError: method should be a single
>  character
>  
>  ----------------------------------------------------------------------
>  Ran 210 tests in 293.712 seconds
>  
>  FAILED (failures = 1)
>  
>  
>  On sparc[3]
>  there is a problem with dialign but sparc is no release
>  architecture and wie might ignore this.  It
>  might be a helpful hint
>  anyway.
>  
>  Any hint for the test_Cluster
>  problem?  If not I would also consider to
>  hide it cowardly under the carpet for the
>  moment.  The new package is so
>  much better
>  tested than the one in the testing distribution which
>  does
>  not even dare about any unit tests and
>  only for this reason reached the
>  testing
>  distribution.
>  
>  What do you
>  think?
>  
>  Kind regards
>  
>     
>     Andreas.
>  
>  scrool these links to the end to see the
>  problem:
>  
>  [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=powerpc&ver=1.64%2Bdfsg-3&stamp=1408116532
>  [2] https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=s390x&ver=1.64%2Bdfsg-3&stamp=1408107524
>  [3]
>  https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=sparc&ver=1.64%2Bdfsg-3&stamp=1408130792
>  
>  -- 
>  http://fam-tille.de
> 
> 

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